Journal
GUT MICROBES
Volume 5, Issue 2, Pages 192-201Publisher
TAYLOR & FRANCIS INC
DOI: 10.4161/gmic.28442
Keywords
neonatal microbiome; host-microbial interactions; fecal microbiome; intestinal bacterial diversity; mucosal immunity
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Funding
- American Academy of Pediatrics Marshall Klaus Perinatal Research Award
- Eunice Kennedy Shriver National Institute Of Child Health and Human Development (NICHD) [T32HD068256, K08HD061607]
- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) [K08DK090146]
- National Science Foundation [DEB-1046149]
- Vanderbilt Digestive Disease Research Center [P30DK058404]
- Vanderbilt Diabetes Center Grant (NIDDK) [P30DK20593]
- Vanderbilt CTSA Grant from the National Center for Research Resources (NCRR) [UL1 RR024975-01]
- Vanderbilt CTSA Grant from the National Center for Research Resources (NIH) [UL1 RR024975-01]
- Vanderbilt Diabetes Center Grant (NIH) [P30DK20593]
- Direct For Biological Sciences [1046149] Funding Source: National Science Foundation
- EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH & HUMAN DEVELOPMENT [T32HD068256, K08HD061607] Funding Source: NIH RePORTER
- NATIONAL CENTER FOR RESEARCH RESOURCES [UL1RR024975] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES [K08DK090146, P30DK020593, P30DK058404] Funding Source: NIH RePORTER
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Fecal sampling is widely utilized to define small intestinal tissue-level microbial communities in healthy and diseased newborns. However, this approach may lead to inaccurate assessments of disease or therapeutics in newborns because of the assumption that the taxa in the fecal microbiota are representative of the taxa present throughout the gastrointestinal tract. To assess the stratification of microbes in the newborn gut and to evaluate the probable shortcoming of fecal sampling in place of tissue sampling, we simultaneously compared intestinal mucosa and fecal microbial communities in 15 neonates undergoing intestinal resections. We report three key results. First, when the site of fecal and mucosal samples are further apart, their microbial communities are more distinct, as indicated by low mean Sorensen similarity indices for each patient's fecal and tissue microbiota. Second, two distinct niches (intestinal mucosa and fecal microbiota) are evident by principal component analyses, demonstrating the critical role of sample source in defining microbial composition. Finally, in contrast to adult studies, intestinal bacterial diversity was higher in tissue than in fecal samples. This study represents an unprecedented map of the infant microbiota from intestinal mucosa and establishes discernable biogeography throughout the neonatal gastrointestinal tract. Our results question the reliance on fecal microbiota as a proxy for the developing intestinal microbiota. Additionally, the robust intestinal tissue-level bacterial diversity we detected at these early ages may contribute to the maturation of mucosal immunity.
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